A hierarchical biology concept framework: a tool for course design

A typical undergraduate biology curriculum covers a very large number of concepts and details. We describe the development of a Biology Concept Framework (BCF) as a possible way to organize this material to enhance teaching and learning. Our BCF is hierarchical, places details in context, nests related concepts, and articulates concepts that are inherently obvious to experts but often difficult for novices to grasp. Our BCF is also cross-referenced, highlighting interconnections between concepts. We have found our BCF to be a versatile tool for design, evaluation, and revision of course goals and materials. There has been a call for creating Biology Concept Inventories, multiple-choice exams that test important biology concepts, analogous to those in physics, astronomy, and chemistry. We argue that the community of researchers and educators must first reach consensus about not only what concepts are important to test, but also how the concepts should be organized and how that organization might influence teaching and learning. We think that our BCF can serve as a catalyst for community-wide discussion on organizing the vast number of concepts in biology, as a model for others to formulate their own BCFs and as a contribution toward the creation of a comprehensive BCF.     

The best of both worlds- bringing together cell biology and infection at the Institut Pasteur

Only a profound understanding of the structure and function of cells - either as single units or in the context of tissues and whole organisms - will allow a comprehension of what happens in pathological conditions and provides the means to fight disease. The Cell Biology and Infection (BCI for Biologie Cellulaire et Infection) department was created in 2002 at the Institut Pasteur in Paris to develop a research program under the umbrella of cell biology, infection biology and microbiology. Its visionary ambition was to shape a common framework for cellular microbiology, and to interface the latter with hard sciences like physics and mathematics and cutting-edge technology. This concept, ahead of time, has given high visibility to the field of cellular microbiology and quantitative cell biology, and it has allowed the successful execution of highly interdisciplinary research programs linking a molecular understanding of cellular events with disease. Now, the BCI department embraces additional pathologies, namely cancer and neurodegenerative diseases. Here, we will portray how the integrative research approach of BCI has led to major scientific breakthroughs during the last ten years, and where we see scientific opportunities for the near future.     

Conceptual assessment in the biological sciences: a National Science Foundation-sponsored workshop

Twenty-one biology teachers from a variety of disciplines (genetics, ecology, physiology, biochemistry, etc.) met at the University of Colorado to begin discussions about approaches to assessing students' conceptual understanding of biology. We considered what is meant by a "concept" in biology, what the important biological concepts might be, and how to go about developing assessment items about these concepts. We also began the task of creating a community of biologists interested in facilitating meaningful learning in biology. Input from the physiology education community is essential in the process of developing conceptual assessments for physiology.     

Planning a lab lesson on the law of thermal conduction with learning by preparing to teach design

Lab activities have been innovated and progressed to fulfill the purpose that students need to experience physics concepts through hands-on and minds-on interactions. However, student-centered and conceptual activities in physics labs are challenged with time and material constraints that degrades the merits of the learning environment. This study adopts a pedagogical design, “learning by preparing to teach”, to address the challenges with conducting a satisfactory number of activities in physics labs and therefore promoting student hands-on and minds-on experiences with the activities. Eight activities covering the conceptual variables of thermal conduction in a two-hour lab session were studied by freshmen students at a university. To implement the pedagogical design, the students were arranged into the learning and teaching groups that paved way to a lab design that student was first learners and then teachers. Lab activities were configured that each group studied a certain set of activities. Upon completing the activities, members of the learning groups were designated to the teaching groups in which students cooperated to achieve conceptual objectives of the lab. The results showed that a usual lab duration becomes effective to cover numerous activities.     

??Are Humans Evolving??? A Classroom Discussion to Change Student Misconceptions Regarding Natural Selection

Natural selection is an important mechanism in the unifying biological theory of evolution, but many undergraduate students struggle to learn this concept. Students enter introductory biology courses with predictable misconceptions about natural selection, and traditional teaching methods, such as lecturing, are unlikely to dispel these misconceptions. Instead, students are more likely to learn natural selection when they are engaged in instructional activities specifically designed to change misconceptions. Three instructional strategies useful for changing student conceptions include (1) eliciting na?ve conceptions from students, (2) challenging nonscientific conceptions, and (3) emphasizing conceptual frameworks throughout instruction. In this paper, we describe a classroom discussion of the question “Are humans evolving?” that employs these three strategies for teaching students how natural selection operates. Our assessment of this activity shows that it successfully elicits students’ misconceptions and improves student understanding of natural selection. Seventy-eight percent of our students who began this exercise with misconceptions were able to partially or completely change their misconceptions by the end of this discussion. The course that this activity was part of also showed significant learning gains (d = 1.48) on the short form of the Conceptual Inventory of Natural Selection. This paper includes all the background information, data, and visual aids an instructor will need to implement this activity.     

Development and Validation of the Food-Craving Inventory

Objective: The primary aim of this study was to develop and validate the Food-Craving Inventory (FCI), a self-report measure of specific food cravings. Research Methods and Procedures: In a preliminary study, participants (n = 474) completed the initial version of the FCI. The results from this study were used in developing the revised FCI. Participants (n = 379) completed the revised FCI in the primary study designed to develop a self-report measure of specific food cravings. Results: Common factor analysis yielded four conceptual factors (subscales) that were interpreted as high fats, sweets, carbohydrates/starches, and fast-food fats. Confirmatory factor analysis found that the four factors could be modeled as dimensions (or first-order factors) of a higher order construct—food craving. Test–retest and internal consistency analyses indicated good reliability for the total score and each of the subscales. Subscale scores were compared with scores on the Three Factor Eating Questionnaire and a conceptual measure of food craving. We found support for the content, concurrent, construct, and discriminant validity of the FCI. Discussion: The FCI was found to be a reliable and valid measure of general and specific food cravings. The FCI can be used in research related to overeating and binge eating. Also, it may be useful in treatment studies that target obesity and/or food cravings.     

Student construction of phylogenetic trees in an introductory biology course

Background

Phylogenetic trees have become increasingly essential across biology disciplines. Consequently, learning about phylogenetic trees has become an important component of biology education and an area of interest for biology education research. Construction tasks, in which students generate phylogenetic trees from some type of data, are often used for instruction. However, the impact of these exercises on student learning is uncertain, in part due to our fragmented knowledge of what students construct during the tasks. The goal of this project was to develop a more robust method for describing student-generated phylogenetic trees, which will support future investigations that attempt to link construction tasks with student learning.

Results

Through iterative examination of data from an introductory biology course, we developed a method for describing student-generated phylogenetic trees in terms of style, conventionality, and accuracy. Students used the diagonal style more often than the bracket style for construction tasks. The majority of phylogenetic trees were constructed conventionally, and variable orientation of branches was the most common unconventional feature. In addition, the majority of phylogenetic trees were generated correctly (no errors) or adequately (minor errors only) in terms of accuracy. Suggesting extant taxa are descended from other extant taxa was the most common major error, while empty branches and extra nodes were very common minor errors.

Conclusions

The method we developed to describe student-constructed phylogenetic trees uncovered several trends that warrant further investigation. For example, while diagonal and bracket phylogenetic trees contain equivalent information, student preference for using the diagonal style could impact comprehension. In addition, despite a lack of explicit instruction, students generated phylogenetic trees that were largely conventional and accurate. Surprisingly, accuracy and conventionality were also dependent on each other. Our method for describing phylogenetic trees constructed by students is based on data from one introductory biology course at one institution, and the results are likely limited. We encourage researchers to use our method as a baseline for developing a more generalizable tool, which will support future investigations that attempt to link construction tasks with student learning.

     

Foundations of form and function: A synthesis‐based curriculum for introductory‐level organismal biology

First‐year majors organismal biology courses are frequently taught as survey courses that promote memorization rather than synthesis of biological concepts. To address the shortcomings of this approach, we redesigned the organismal portion of our introductory biology curriculum to create a “Foundations of Form and Function” course. Foundations of Form and Function introduces different organismal forms and focuses on the relationship between those forms and the execution of key physiological functions. Goals of our new course include the following: developing student recognition of common characteristics that unite living organisms as well as features that distinguish taxonomic groups, facilitating student understanding of how organisms accomplish similar functions through different forms, and reinforcing course themes with independent student research. In this paper, we describe course learning outcomes, organization, content, assessment, and laboratory activities. We also present student perspectives and outcomes of our course design based on data from four years of student evaluations. Finally, we explain how we modified our course to meet remote learning and social‐distancing challenges presented by the COVID‐19 pandemic in 2020 and 2021.     

Enhancing theoretical understanding of a practical biology course using active and self-directed learning strategies

Laboratories are recognised as central in science education, allowing students to consolidate knowledge and master practical skills, however, their effectiveness has been questioned. Whilst laboratory practicals are useful for students’ learning of basic procedures, they have been shown to be less effective for developing conceptual understanding of the subject. Interactive lectures and bespoke digital resources were utilised in order to enhance theoretical understanding of laboratory practical molecular sessions, thus enabling students to take responsibility for and direct their own learning, encouraging inquiry-based learning. Providing easy to access additional learning resources offered students an opportunity to better prepare themselves for the laboratory, and consolidate their knowledge through subsequent review and self-testing in their own time. Grades before and after implementation of these active learning strategies were analysed to look at the impact on student learning and this study demonstrates that integrating these into a challenging practical biology course improved grades significantly with a concomitant increase in the number of ‘A’ grades attained. Feedback to evaluate use and perceptions of both interactive lectures and digital resources were also analysed. It has been shown here that these activities enhanced student experience and understanding of the course.     

Not Looking a Gift Horse in the Mouth: Exploring the Merits of a Student–Teacher–Scientist Partnership

One major emphasis of reform initiatives in science education is the importance of extended inquiry experiences for students through authentic collaborations with scientists. As such, unique partnerships have started to emerge between science and education in an ongoing effort to capture the interest and imaginations of students as they make sense of the world around them. One such partnership is called the student–teacher–scientist partnership, in which teachers and their students participate in and contribute to the research of scientists. This article explores a partnership between a 10th-grade biology teacher, her students, and practicing scientists who collaborated in the design, implementation and evaluation of a horse evolution unit. The primary goal of the collaborative activity was to involve teachers and students in a process of conceptual change as a means of eliminating common misconceptions implicit in horse evolution displays in museums in various parts of the country. The evidence-based lessons developed enhanced students’ understanding of concepts in macroevolution but also connected the science classroom with a community of scientists whose personalization of the horse evolution unit situated biological concepts and the learning experience within the context of real-world issues.     

Teachers' journal club: bridging between the dynamics of biological discoveries and biology teachers

Since biology is one of the most dynamic research fields within the natural sciences, the gap between the accumulated knowledge in biology and the knowledge that is taught in schools, increases rapidly with time. Our long-term objective is to develop means to bridge between the dynamics of biological discoveries and the biology teachers and students. Here we report on our recent initiative towards this objective in which we established a journal club forum as a means towards the professional development of biology teachers. We used the journal club format, which is common within the scientific community, in order to engage biology teachers in a constructivist type of learning in which they acquire new skills and at the same time are continuously updated as to biological discoveries, and can then develop updated activities for their biology students. We suggest using the journal club format for the long-term professional development of biology teachers.     

Using case-study based modules to promote a better understanding of evolution in an undergraduate anatomy and physiology course

ABSTRACT

The impact of evolutionary processes in understanding human health and disease is an important idea for future health professionals to understand. These students, however, typically receive little to no formal instruction in the role of evolution in not only understanding human health, but its impact on how to treat human diseases. To address this issue, we developed and implemented a case-study based learning module designed with a learning cycle implementation as part of a larger evolution across the curriculum program. The module focused on the evolution of skin color to illustrate that natural selection occurs in humans, and that the process of evolution involves tradeoffs (a balance of costs and benefits). Student understanding of the tradeoffs of natural selection was assessed through a pre- post- test design, with students answering a set of questions before instruction and again after. The modules helped improve student comprehension of natural selection, particularly for lower-performing students who were not biology majors, and for those whom reported less interest in evolution.     

Teaching more by lecturing less

We carried out an experiment to determine whether student learning gains in a large, traditionally taught, upper-division lecture course in developmental biology could be increased by partially changing to a more interactive classroom format. In two successive semesters, we presented the same course syllabus using different teaching styles: in fall 2003, the traditional lecture format; and in spring 2004, decreased lecturing and addition of student participation and cooperative problem solving during class time, including frequent in-class assessment of understanding. We used performance on pretests and posttests, and on homework problems to estimate and compare student learning gains between the two semesters. Our results indicated significantly higher learning gains and better conceptual understanding in the more interactive course. To assess reproducibility of these effects, we repeated the interactive course in spring 2005 with similar results. Our findings parallel results of similar teaching-style comparisons made in other disciplines. On the basis of this evidence, we propose a general model for teaching large biology courses that incorporates interactive engagement and cooperative work in place of some lecturing, while retaining course content by demanding greater student responsibility for learning outside of class.     

Anticipation of Personal Genomics Data Enhances Interest and Learning Environment in Genomics and Molecular Biology Undergraduate Courses

An important discussion at colleges is centered on determining more effective models for teaching undergraduates. As personalized genomics has become more common, we hypothesized it could be a valuable tool to make science education more hands on, personal, and engaging for college undergraduates. We hypothesized that providing students with personal genome testing kits would enhance the learning experience of students in two undergraduate courses at Brigham Young University: Advanced Molecular Biology and Genomics. These courses have an emphasis on personal genomics the last two weeks of the semester. Students taking these courses were given the option to receive personal genomics kits in 2014, whereas in 2015 they were not. Students sent their personal genomics samples in on their own and received the data after the course ended. We surveyed students in these courses before and after the two-week emphasis on personal genomics to collect data on whether anticipation of obtaining their own personal genomic data impacted undergraduate student learning. We also tested to see if specific personal genomic assignments improved the learning experience by analyzing the data from the undergraduate students who completed both the pre- and post-course surveys. Anticipation of personal genomic data significantly enhanced student interest and the learning environment based on the time students spent researching personal genomic material and their self-reported attitudes compared to those who did not anticipate getting their own data. Personal genomics homework assignments significantly enhanced the undergraduate student interest and learning based on the same criteria and a personal genomics quiz. We found that for the undergraduate students in both molecular biology and genomics courses, incorporation of personal genomic testing can be an effective educational tool in undergraduate science education.     

Time Development in the Early History of Social Networks: Link Stabilization,Group Dynamics,and Segregation

Studies of the time development of empirical networks usually investigate late stages where lasting connections have already stabilized. Empirical data on early network history are rare but needed for a better understanding of how social network topology develops in real life. Studying students who are beginning their studies at a university with no or few prior connections to each other offers a unique opportunity to investigate the formation and early development of link patterns and community structure in social networks. During a nine week introductory physics course, first year physics students were asked to identify those with whom they communicated about problem solving in physics during the preceding week. We use these students'' self reports to produce time dependent student interaction networks. We investigate these networks to elucidate possible effects of different student attributes in early network formation. Changes in the weekly number of links show that while roughly half of all links change from week to week, students also reestablish a growing number of links as they progress through their first weeks of study. Using the Infomap community detection algorithm, we show that the networks exhibit community structure, and we use non-network student attributes, such as gender and end-of-course grade to characterize communities during their formation. Specifically, we develop a segregation measure and show that students structure themselves according to gender and pre-organized sections (in which students engage in problem solving and laboratory work), but not according to end-of-coure grade. Alluvial diagrams of consecutive weeks'' communities show that while student movement between groups are erratic in the beginnning of their studies, they stabilize somewhat towards the end of the course. Taken together, the analyses imply that student interaction networks stabilize quickly and that students establish collaborations based on who is immediately available to them and on observable personal characteristics.     

Growing Bayesian network models of gene networks from seed genes

MOTIVATION: For the last few years, Bayesian networks (BNs) have received increasing attention from the computational biology community as models of gene networks, though learning them from gene-expression data is problematic. Most gene-expression databases contain measurements for thousands of genes, but the existing algorithms for learning BNs from data do not scale to such high-dimensional databases. This means that the user has to decide in advance which genes are included in the learning process, typically no more than a few hundreds, and which genes are excluded from it. This is not a trivial decision. We propose an alternative approach to overcome this problem. RESULTS: We propose a new algorithm for learning BN models of gene networks from gene-expression data. Our algorithm receives a seed gene S and a positive integer R from the user, and returns a BN for the genes that depend on S such that less than R other genes mediate the dependency. Our algorithm grows the BN, which initially only contains S, by repeating the following step R + 1 times and, then, pruning some genes; find the parents and children of all the genes in the BN and add them to it. Intuitively, our algorithm provides the user with a window of radius R around S to look at the BN model of a gene network without having to exclude any gene in advance. We prove that our algorithm is correct under the faithfulness assumption. We evaluate our algorithm on simulated and biological data (Rosetta compendium) with satisfactory results.     

Nicolas Rashevsky's Mathematical Biophysics

This paper explores the work of Nicolas Rashevsky, a Russian émigré theoretical physicist who developed a program in “mathematical biophysics” at the University of Chicago during the 1930s. Stressing the complexity of many biological phenomena, Rashevsky argued that the methods of theoretical physics – namely mathematics – were needed to “simplify” complex biological processes such as cell division and nerve conduction. A maverick of sorts, Rashevsky was a conspicuous figure in the biological community during the 1930s and early 1940s: he participated in several Cold Spring Harbor symposia and received several years of funding from the Rockefeller Foundation. However, in contrast to many other physicists who moved into biology, Rashevsky's work was almost entirely theoretical, and he eventually faced resistance to his mathematical methods. Through an examination of the conceptual, institutional, and scientific context of Rashevsky's work, this paper seeks to understand some of the reasons behind this resistance. This revised version was published online in July 2006 with corrections to the Cover Date.     

Using Avida-ED for Teaching and Learning About Evolution in Undergraduate Introductory Biology Courses

Evolution is a complex subject that requires knowledge of basic biological concepts and the ability to connect them across multiple scales of time, space, and biological organization. Avida-ED is a digital evolution educational software environment designed for teaching and learning about evolution and the nature of science in undergraduate biology courses. This study describes our backward design approach to developing an instructional activity using Avida-ED for teaching and learning about evolution in a large-enrollment introductory biology course. Using multiple assessment instruments, we measured student knowledge and understanding of key principles of natural selection before and after instruction on evolution (including the Avida-ED activity). Assessment analysis revealed significant post-instruction learning gains, although certain evolutionary principles (most notably those including genetics concepts, such as the genetic origin of variation) remained particularly difficult for students, even after instruction. Students, however, demonstrated a good grasp of the genetic component of the evolutionary process in the context of a problem on Avida-ED. We propose that: (a) deep understanding of evolution requires complex systems thinking skills, such as connecting concepts across multiple levels of biological organization, and (b) well designed use of Avida-ED holds the potential to help learners build a meaningful and transferable understanding of the evolutionary process. An erratum to this article can be found at     

Models in biology: form and function

The relationships between physical and biological sciences are important in science education. This is shown in the links between the structure of biological science and the use of models. Although the physical sciences contain many principles of wide application, much of biology consists of very distinct examples. When these examples are used as models of organisms or processes, misunderstanding can occur if the characteristics of the model are used to make inaccurate generalizations. In biological education, stress on the importance of unique features must continually accompany the demonstration of similarities.

Theoretical models are constructed and reconstructed by students learning science, particularly in relation to broadly applicable principles. In biology a student may build a theoretical model of a subject which is itself a model used as an example. Distinct features of biological science may influence a variety of learning situations including problem solving.     

Comparing biology majors from large lecture classes with TA-facilitated laboratories to those from small lecture classes with faculty-facilitated laboratories

The teaching faculty for this course sought to address their own concerns about the quality of student learning in an impersonal large lecture biology class for majors, the difficulties in getting to know each student by name, and difficulties in soliciting answers and reactions from the students during the lecture. Questions addressed by this study were, Do active-learning activities in a small and personal lecture setting enhance student learning more than active-learning activities in large impersonal lectures? and Are students more satisfied with an educational experience in a small and personal lecture setting? Based on faculty perceptions of how they best relate to their students, the prediction was that the students in the experimental group with small lecture classes and increased direct contact with the teaching faculty would learn physiological principles better than the students in the control group in the large impersonal lecture portion of the course. One of the laboratory sections of this large enrollment biology course was randomly selected to be taught with separate small lectures by the teaching faculty. In addition, the teaching faculty participated in the laboratory with these students during their experiments correlated with the lecture material. The students in both groups were compared by pre- and posttests of physiological principles, final course grades, and class satisfaction surveys.